Suspended algae, or phytoplankton, are the prime source of organic matter supporting food webs in freshwater ecosystems. Phytoplankton productivity is reliant on adequate nutrient supplies; however, increasing rates of nutrient supply, much of it manmade, fuels accelerating primary production or eutrophication. An obvious and problematic symptom of eutrophication is rapid growth and accumulations of phytoplankton, leading to discoloration of affected waters. These events are termed blooms. Blooms are a prime agent of water quality deterioration, including foul odors and tastes, deoxygenation of bottom waters (hypoxia and anoxia), toxicity, fish kills, and food web alterations. Toxins produced by blooms can adversely affect animal (including human) health in waters used for recreational and drinking purposes. Numerous freshwater genera within the diverse phyla comprising the phytoplankton are capable of forming blooms; however, the blue-green algae (or cyanobacteria) are the most notorious bloom formers. This is especially true for harmful toxic, surface-dwelling, scum-forming genera (e.g., Anabaena, Aphanizomenon, Nodularia, Microcystis) and some subsurface bloom-formers (Cylindrospermopsis, Oscillatoria) that are adept at exploiting nutrient-enriched conditions. They thrive in highly productive waters by being able to rapidly migrate between radiance-rich surface waters and nutrient-rich bottom waters. Furthermore, many harmful species are tolerant of extreme environmental conditions, including very high light levels, high temperatures, various degrees of desiccation, and periodic nutrient deprivation. Some of the most noxious cyanobacterial bloom genera (e.g., Anabaena, Aphanizomenon, Cylindrospermopsis, Nodularia) are capable of fixing atmospheric nitrogen (N2), enabling them to periodically dominate under nitrogen-limited conditions. Cyanobacteria produce a range of organic compounds, including those that are toxic to higher-ranked consumers, from zooplankton to further up the food chain. Both N2- and non-N2-fixing genera participate in mutualistic and symbiotic associations with microorganisms, higher plants, and animals. These associations appear to be of great benefit to their survival and periodic dominance. In this review, we address the ecological impacts and environmental controls of harmful blooms, with an emphasis on the ecology, physiology, and management of cyanobacterial bloom taxa. Combinations of physical, chemical, and biotic features of natural waters function in a synergistic fashion to determine the sensitivity of water bodies. In waters susceptible to blooms, human activities in water- and airsheds have been linked to the extent and magnitudes of blooms. Control and management of cyanobacterial and other phytoplankton blooms invariably includes nutrient input constraints, most often focused on nitrogen (N) and/or phosphorus (P). The types and amount of nutrient input constraints depend on hydrologic, climatic, geographic, and geologic factors, which interact with anthropogenic and natural nutrient input regimes. While single nutrient input constraints may be effective in some water bodies, dual N and P input reductions are usually required for effective long-term control and management of harmful blooms. In some systems where hydrologic manipulations (i.e., plentiful water supplies) are possible, reducing the water residence time by enhanced flushing and artificial mixing (in conjunction with nutrient input constraints) can be particularly effective alternatives. Implications of various management strategies, based on combined ecophysiological and environmental considerations, are discussed.

Oceanic Nitrogen Fixation: Nitrogen fixation in the oceans is important in sustaining global marine productivity and balances carbon dioxide export to the deep ocean. It was previously believed that marine nitrogen fixation was due to a single genus of filamentous cyanobacteria, Trichodesmium . The recent discovery of unicellular open-ocean cyanobacteria has raised the question of how they contribute to global ocean nitrogen fixation and how they compare in distribution and activity to Trichodesmium . Using data collected from the southwest Pacific Ocean, Moisander et al. (p. 1512 , published online 25 February) show that the unicellular nitrogen-fixing cyanobacteria (UCYN-A and Crocosphaera watsonii ) have distinct ecophysiologies and distinct oceanic distributions from each other, and from Trichodesmium . These data can be incorporated into models to retune estimates of the global rates of oceanic nitrogen fixation and carbon sequestration.

Marine N₂ fixing microorganisms, termed diazotrophs, are a key functional group in marine pelagic ecosystems. The biological fixation of dinitrogen (N₂) to bioavailable nitrogen provides an important new source of nitrogen for pelagic marine ecosystems and influences primary productivity and organic matter export to the deep ocean. As one of a series of efforts to collect biomass and rates specific to different phytoplankton functional groups, we have constructed a database on diazotrophic organisms in the global pelagic upper ocean by compiling about 12 000 direct field measurements of cyanobacterial diazotroph abundances (based on microscopic cell counts or qPCR assays targeting the nifH genes) and N₂ fixation rates. Biomass conversion factors are estimated based on cell sizes to convert abundance data to diazotrophic biomass. The database is limited spatially, lacking large regions of the ocean especially in the Indian Ocean. The data are approximately log-normal distributed, and large variances exist in most sub-databases with non-zero values differing 5 to 8 orders of magnitude. Reporting the geometric mean and the range of one geometric standard error below and above the geometric mean, the pelagic N₂ fixation rate in the global ocean is estimated to be 62 (52–73) Tg N yr⁻¹ and the pelagic diazotrophic biomass in the global ocean is estimated to be 2.1 (1.4–3.1) Tg C from cell counts and to 89 (43–150) Tg C from nifH-based abundances. Reporting the arithmetic mean and one standard error instead, these three global estimates are 140 ± 9.2 Tg N yr⁻¹, 18 ± 1.8 Tg C and 590 ± 70 Tg C, respectively. Uncertainties related to biomass conversion factors can change the estimate of geometric mean pelagic diazotrophic biomass in the global ocean by about ±70%. It was recently established that the most commonly applied method used to measure N₂ fixation has underestimated the true rates. As a result, one can expect that future rate measurements will shift the mean N₂ fixation rate upward and may result in significantly higher estimates for the global N₂ fixation. The evolving database can nevertheless be used to study spatial and temporal distributions and variations of marine N₂ fixation, to validate geochemical estimates and to parameterize and validate biogeochemical models, keeping in mind that future rate measurements may rise in the future. The database is stored in PANGAEA (doi:10.1594/PANGAEA.774851).

We report on the contamination of commercial 15-nitrogen (¹⁵N) N₂ gas stocks with ¹⁵N-enriched ammonium, nitrate and/or nitrite, and nitrous oxide. ¹⁵N₂ gas is used to estimate N₂ fixation rates from incubations of environmental samples by monitoring the incorporation of isotopically labeled ¹⁵N₂ into organic matter. However, the microbial assimilation of bioavailable ¹⁵N-labeled N₂ gas contaminants, nitrate, nitrite, and ammonium, is liable to lead to the inflation or false detection of N₂ fixation rates. ¹⁵N₂ gas procured from three major suppliers was analyzed for the presence of these ¹⁵N-contaminants. Substantial concentrations of ¹⁵N-contaminants were detected in four Sigma-Aldrich ¹⁵N₂ lecture bottles from two discrete batch syntheses. Per mole of ¹⁵N₂ gas, 34 to 1900 µmoles of ¹⁵N-ammonium, 1.8 to 420 µmoles of ¹⁵N-nitrate/nitrite, and ≥21 µmoles of ¹⁵N-nitrous oxide were detected. One ¹⁵N₂ lecture bottle from Campro Scientific contained ≥11 µmoles of ¹⁵N-nitrous oxide per mole of ¹⁵N₂ gas, and no detected ¹⁵N-nitrate/nitrite at the given experimental ¹⁵N₂ tracer dilutions. Two Cambridge Isotopes lecture bottles from discrete batch syntheses contained ≥0.81 µmoles ¹⁵N-nitrous oxide per mole ¹⁵N₂, and trace concentrations of ¹⁵N-ammonium and ¹⁵N-nitrate/nitrite. ¹⁵N₂ gas equilibrated cultures of the green algae Dunaliella tertiolecta confirmed that the ¹⁵N-contaminants are assimilable. A finite-differencing model parameterized using oceanic field conditions typical of N₂ fixation assays suggests that the degree of detected ¹⁵N-ammonium contamination could yield inferred N₂ fixation rates ranging from undetectable, <0.01 nmoles N L⁻¹ d⁻¹, to 530 nmoles N L⁻¹ d⁻¹, contingent on experimental conditions. These rates are comparable to, or greater than, N₂ fixation rates commonly detected in field assays. These results indicate that past reports of N₂ fixation should be interpreted with caution, and demonstrate that the purity of commercial ¹⁵N₂ gas must be ensured prior to use in future N₂ fixation rate determinations.

Human encroachment on aquatic ecosystems is increasing at an unprecedented rate. The impacts of human pollution and habitat alteration are most evident and of greatest concern at the microbial level, where a bulk of production and nutrient cycling takes place. Aquatic ecosystems are additionally affected by natural perturbations, including droughts, storms, and floods, the frequency and extent of which may be increasing. Distinguishing and integrating the impacts of natural and human stressors is essential for understanding environmentally driven change of microbial diversity and function. Microbial bioindicators play a major role in detecting and characterizing these changes. Complementary use of analytical and molecular indicator tools shows great promise in helping us clarify the processes underlying microbial population, community, and ecosystem change in response to environmental perturbations. This is illustrated in phytoplankton (microalgal and cyanobacterial) and bacterial community changes in a range of US estuarine and coastal ecosystems experiencing increasing development in their water- and airsheds as well as climatic changes (e.g., increasing hurricane frequency). Microbial indicators can be adapted to a range of monitoring programs, including ferries, moored instrumentation, and remote sensing, in order to evaluate environmental controls on microbial community structure and function over ecosystem to global scales.

The spatial heterogeneity of diversity and abundance of diazotrophs were investigated off the Vietnamese coast in the South China Sea (SCS). The study area extended from the Mekong River plume to the shelf region and beyond to stations extending to 1700 m depth. The SCS diazotroph community, based on nifH gene diversity, had components closely related to sequences from open ocean, estuarine, saltmarsh and microbial mat communities. Rarefaction analysis suggested that by using a 97% similarity operational taxonomic unit definition, the majority of nifH sequence diversity in the samples was covered by the 384 nifH clones obtained. The majority of the nifH sequences recovered fell into two clusters: one comprised of Trichodesmium sequences and the other an α-proteobacterial group. Unicellular cyanobacterial groups A and B, and symbiotic filamentous cyanobacterial diazotrophs were detected sporadically. Trichodesmium was by far the most abundant diazotroph, with up to 6 × 10⁵ nifH gene copies per liter. Quantitative PCR probe–primer sets were designed and used to quantify two proteobacterial groups, revealing abundances up to 10³–10⁴ nifH gene copies per liter, with the highest abundances in the photic zone. Major components of the clone library were also revealed by a nifH microarray and multidimensional scaling (MDS) analysis. MDS showed that samples from the >10 μm size fraction from 0- to 5-m depths clustered separately from the rest of the samples, primarily due to the abundance of Trichodesmium sequences. The SCS diazotroph community has a relatively low diversity and is a mixture of both estuarine and oceanic fingerprints.